The present invention relates to an apparatus and to a method for mapping a three-dimensional space in medical applications for diagnostic, surgical or interventional medicine purposes. The apparatus and the method according to the invention use acquisition means, capable of recording two-dimensional images of said three-dimensional space from at least a first recording position and from a second recording position, and a reference target, comprising a plurality of marker elements and movable between a first target point and a second target point of said three-dimensional space. A processing unit, adapted to receive data indicative of a first image and of a second image of said three-dimensional space, comprises computerized means adapted to calculate registration data to register the two-dimensional reference systems, used to express the coordinates of the points of said first image and of said second image, with the three-dimensional reference system, defined by the marker elements of said reference target.